Jeremy, I got it working. Thanks ---------- Forwarded message ---------- From: shamsher jagat <kanwar...@gmail.com>o Date: Mon, May 16, 2011 at 4:19 PM Subject: problem with filter RNA-seq To: jeremy.goe...@emory.edu Cc: galaxy-u...@bx.psu.edu
I have tried to follow the steps: File 33 in my history is generated by using filter GTF data by attributes. Two files used were file 29 which is a splicing diff file filtered for yes and file 2 is combined GTF. I used TSS-id for filtering. the out put file file 32 is empty. Any suggestion? Jagat, It depends what filter tool you're using and what dataset you're filtering. There is a generic filter tool that can be used to filter Cuffdiff tabular files for either FPKM values and differential expression tests. There is also a tool for filtering GTF files based on a Cuffdiff expr dataset. It sounds like you may be confusing either the tools or the inputs. If after double-checking you're still having problems with filtering, please put together a short list of your analysis steps and share your history with me, and I can take a look. Thanks, J. Further to my question, It appear that there is some problem with the filter option: When I use the isoform/gene exp file as such it work fine but when I filter these files with either parameter such as status if test was successful or on p value it return me empty file. The way am saving the file is - expr file filter save as txt file and upload back in Galaxy. Any suggestion? Jagat
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
